Phylogenetic dating of HIV latency
Jones BR, Kinloch NN, Horacsek J, Ganase B, Harris M, Harrigan PR, Jones RB, Brockman M, Joy JB, Poon FY Brumme ZL. (2018) Phylogenetic approach to recover integration dates of latent HIV sequences within-host. Proceedings of the National Academy of Sciences USA 115(38):E8958-E8967.
Jones B, Kinloch N, Horacsek J, Ganase B, Harris M, Harrigan PR, Jones BR, Brockman M, Joy J, Poon A, Brumme Z. Using phylogenetics to reconstruct the integration dates of individual latent human immunodeficiency virus reservoir sequences. The 2nd Symposium of the Canadian Society for Virology (2018, Halifax Canada) abstract 42.
Jones BR, Kinloch NN, Horacsek J, Ganase B, Harris M, Jones RB, Harrigan PR, Brockman MA, Joy JB, Poon A, Brumme ZL. A Phylogenetic Approach to Recover Integration Dates of Latent Human Immunodeficiency Virus Sequences Within-Host. 27th Annual Canadian Conference on HIV / AIDS Research (2018, Vancouver, Canada) abstract BSP4.03.
Jones BR, Kinloch NN, Horacsek J, Ganase B, Harris M, Jones RB, Harrigan PR, Brockman MA, Joy JB, Poon A, Brumme ZL. Reconstructing intergation of dates of latent HIV sequences within-host. The Conference on Retroviruses and Opportunistic Infections 2018 (2018, Boston, United States of America) abstract 372.
Jones BR, Kinloch NN, Horacsek J, Ganase B, Harris M, Jones RB, Harrigan PR, Brockman MA, Joy JB, Poon A, Brumme ZL. The latent reservoir as a genetically diverse archive recapitulating within-host HIV evolutionary history. HIV Persistance during Therapy 8th Edition (2017, Miami, United States of America) abstract 00035.
Jones BR, Kinloch NN, Horacsek J, Mwimanzi P, Huang J, Truong R, Ganase B, Harris M, Harrigan PR, Jones RB, Brockman MA, Joy JB, Poon A, Brumme ZL. Heterogeneous age and genetic distribution of within-host HIV-1 reservoirs revealed by a novel phylogenetic dating strategy. 9th IAS Conference on HIV Science (2017, Paris, France) abstract MOPEA0004.
Jones BR, Kinloch NN, Horacsek J, Mwimanzi P, Huang J, Truong R, Ganase B, Harris M, Harrigan PR, Jones RB, Brockman MA, Joy JB, Poon A, Brumme ZL. The HIV reservoir as a genetically heterogeneous archive of within-host viral evolution: implications for immunotherapeutic cure strategies. IAS HIV Cure & Cancer Forum (2017, Paris, France) abstract P22.
Jones BR, Horacsek J, Joy JB, Brumme ZL, Poon AFY. Blind-dating: using phlylogeny to find the ages of latent HIV-1 sequences within host. 24th Conference on Retroviruses and Opportunistic Infections (2017, Seattle, United States of America) abstract 196.
Jones BR, Horacsek J, Joy JB, Brumme ZL, Poon AFY. Blind dating: a phylogenetic approach to dating HIV reservoir sequences. The 25th Annual Canadian Conference on HIV/AIDS Research (2016, Winnipeg, Canada) abstract BSP3.06.
Blind-dating also requires RAxML. Python3 and INDELible are needed for the simulations only.